Journal of clinical virology plus最新文献

Objective

To investigate whether SARS-CoV-2 omicron breakthrough infection in individuals after three doses of wildtype-based BNT162b2 increases antibody levels measured by a commercially available wildtype-based immunoassay.

Methods

16 of 21 individuals in a BNT162b2 vaccination cohort (recruited 129 [129–135] days after dose 3) experienced a breakthrough infection (BTI) between March and September 2022. Antibodies to the receptor binding domain (RBP) of the spike protein (Anti-S) were quantified using the wildtype-based Elecsys SARS-CoV-2 S assay (Roche). Antibody responses of triple vaccinated BTI cases were compared to triple vaccinated individuals without breakthrough infection and to 16 matched individuals after primary omicron infection.

Results

In the 16 individuals with primary Omicron infection, the anti-S assay returned only very low results (2.25 [0.61–5.80] U/mL). However, in individuals with BTI, Anti-S levels rose from 7,135 [5,870–17,470] U/mL to 21,705 (7,750–46,137.5) U/mL. At the same time, Anti-S concentrations decreased from 9,120 [7,480–13,480] U/mL to 3,830 (2,390–4,220) U/mL in those 5 of 21 vaccinated only.

Conclusions

Our data suggest that breakthrough infection with omicron can efficiently boost wild-type antibodies in individuals vaccinated with wild-type BNT162b2.

Background

The role of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) neutralizing antibody response from natural infection and vaccination, and the potential determinants of this response are poorly understood. Characterizing this antibody response and the factors associated with neutralization can help inform future prevention efforts and improve clinical outcomes in those infected.

Objectives

The goals of this study were to prospectively evaluate SARS-CoV-2 antibody levels and the neutralizing antibody responses among naturally infected adults and to determine demographic and behavioral factors independently associated with these responses.

Methods

Serum was collected from seropositive individuals at baseline, four-weeks, and three-months following their first study visit to be evaluated for antibody levels. Detection of neutralizing antibodies was performed at baseline. Participant demographic and behavioral information was collected via web questionnaire prior to their first visit.

Results

At baseline, higher antibody levels were associated with better neutralization capacity, with 83% of participants having detectable neutralizing antibodies. We found an age-dependent effect on antibody level and neutralization capacity with participants over 65 years having significantly higher levels. Ethnicity, heart disease, autoimmune disease, and COVID symptoms were associated with higher antibody levels, but not with increased neutralization capacity. Work environment during the pandemic correlated with increased neutralization capacity, while kidney or liver disease and traveling out of state after February 2020 correlated with decreased neutralization capacity, however neither correlated with antibody levels.

Conclusions

Our data show that natural infection by SARS-CoV-2 can induce a humoral response reflected by high antibody levels and neutralization capacity.

Background

Human respiratory syncytial virus (HRSV) is an important pathogen causing severe acute respiratory infection (SARI), particularly in children under 5 years old. We investigated the HRSV infection status and genogroups in pediatric patients with SARI between January 2019 and December 2022 in Huzhou, China.

Methods

Nasopharyngeal swabs (NPSs) were collected from pediatric patients in the First People's Hospital of Huzhou. Real-time quantitative RT-PCR for respiratory syncytial virus (A/B)was performed with an QuantStudio 7 Flex Real-Time PCR System. For genotyping, the primer sets A-F/A-R and B-F/B-R were used to amplify the G protein sequences of HRSV-A and HRSV-B, respectively. Phylogenetic analysis was performed using MEGA software.

Results

In total, 973 NPSs were collected between January 2019 and December 2022, and 63 samples were positive for HRSV nucleic acid, representing a detection rate of 6.47%. Of the positive specimens, 28 were classified as HRSV-A and 35 were classified as HRSV-B. Infection with HRSV was found in all age groups tested, with children < 5 years old accounting for 88.89% of the positive cases. The detection rate was high from November to the following March. Phylogenetic analysis clustered HRSV-A strains into the ON1 genogroup and HRSV-B strains belonged to the BA9 genogroup.

Conclusions

HRSV is an important respiratory pathogen among children in Huzhou, China, with a high incidence in children under 5 years old between winter and spring. HRSV subgroups A and B were co-circulating, and ON1 and BA9 were the two main genogroups identified in this study.

Nucleocapsid gene-positive, envelope gene-negative (N2+/E-) SARS-CoV-2 PCR results obtained with the Cepheid Xpert Xpress SARS-CoV-2 assay are an infrequent phenomenon. We assessed the validity of the N2+/E- cases with an indirect approach by analyzing their occurrence in relation to overall positive PCR rates and absolute number of PCR tests (24,909 samples, collected June 2021 to July 2022). Additionally, 3022 samples were analyzed with the Xpert Xpress CoV-2-plus assay in August/September 2022. The incidence of monthly N2+/E- cases closely followed the overall frequency of positive tests (p < 0.001), while there was no correlation with the monthly number of PCR test. The observed distribution of N2+/E- cases implicates, that they are not merely artefacts, but rather represent samples with a very low viral load. This phenomenon will persist with the Xpert Xpress SARS-CoV-2 plus assay, which also produced more than 10% results where only one target gene replicated with a very high Ct value.

Background

Dengue, ranked as one of the most critical viral diseases, requires rapid, accurate, and early diagnosis for better patient care.

Objectives

This study pertains to the development and clinical validation of an in house easy to do, affordable kit for the detection of dengue NS1 antigen based on lateral flow immunoassay in serum samples of patients.

Study Design

Clinically uncharacterized serum specimens were obtained and analyzed using the developed NS1 detection kit and compared against the ELISA results.

Results

The performance of the kit was evaluated with both positive and negative patients’ serum samples for NS1 antigen and found to be highly specific and sensitive. An overall sensitivity of 92.16 % and specificity of 97.25 % were recorded. Kit stability tests were also carried out and the performance of the kit was found to be similar to real time tests.

Conclusion

The results indicate that the developed NS1 detection kit has good reliability with comparable performance to ELISA results.

Background & Aims The use of direct acting antiviral agents (DAAs) in patients with chronic HCV genotype (GT) 3a infection results in sustained virologic response (SVR) rates of 93–98%, but 5–8% of patients experience virologic failure. Methods. We observed 48 patients infected with HCV subtype 3a who failed previous treatment with DAAs, including 43 subjects (89.6%) with liver cirrhosis. Thirty-seven (77%) subjects previously received NS5A inhibitors of the first generation (daclatasvir) and 11 subjects (23%) – of the second generation (velpatasvir). All patients received retreatment with sofosbuvir (SOF)/ velpatasvir (VEL) and ribavirin (RBV) for 24 weeks. We compared SVR₁₂ rates depending on fibrosis stage, presence of NS5A mutation (L31M or A30K and Y93H), and on the generation of previously used NS5A inhibitors. Results. Observed SVR₁₂ rate were: 83,3% (40/48 patients) overall; 100% in patients without cirrhosis (n=5) vs 81,4% (n=35) in those with cirrhosis (n=43) (P=0,01); 86,7% (n=13) with single L31M or A30K(n=15) vs 77,8% (n=21) with Y93H mutation (n=27) (P=0,46), 86,5% (n=32) in patients who previously failed first generation (n=37) vs 72,7% (n=8) in those who failed second generation NS5A inhibitors (n=11) (P=0,35). Conclusions. Retreatment with SOF/VEL+RBV was highly effective and safe in patients with chronic HCV GT3a infection, including those with liver cirrhosis, who previously failed DAA containing NS5A inhibitors. Presence of NS5A RASs L31M, A30K, and Y93H at the baseline, as well as the generation of previously used NS5A inhibitors did not impact SVR₁₂ rates.

Objectives

Shotgun proteomics is a generic method enabling detection of multiple viral species in one assay. The reliable and accurate identification of these viral species by analyzing peptides from MS-spectra is a challenging task. The aim of this study was to develop an easy accessible proteome analysis approach for the identification of viruses that cause respiratory and gastrointestinal infections.

Methods

For this purpose, a shotgun proteomics based method and a web application, ‘proteome2virus’, were developed. Identified peptides were searched in a database comprising proteomic data of 46 viruses known to be infectious to humans.

Results

The method was successfully tested for cultured viruses and eight fecal samples consisting of ten different viral species from seven different virus families, including SARS-CoV-2. The samples were prepared with two different sample preparation methods and were measured with two different mass spectrometers.

Conclusions

The results demonstrate that the developed web application is applicable to different MS data sets, generated from two different instruments, and that with this approach a high variety of clinically relevant viral species can be identified. This emphasizes the potential and feasibility for the diagnosis of a wide range of viruses in clinical samples with a single shotgun proteomics analysis.